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The na'onal bioinforma'cs infrastructure www.scilifelab.se/pla7orms/bioinforma'cs/
Björn Nystedt, bjorn.nystedt@scilifelab.se Bioinforma'cs Long-‐term Support (a.k.a.WABI)
The Bioinforma'cs pla7orm
SciLifeLab
Na'onal Genomics Infrastructure
Bioinforma'cs
Joakim Lundeberg Ann-‐Chris'ne Syvänen Ulf Gyllensten
Bengt Persson
Clinical Diagnos'cs
…
Ongoing merge of BILS, WABI and more; complete 2016. Na'onal, distributed
Sequencing
NGI
BIOINFORMATICS
Supercomputer center
Genomics development Lab Bioinfo
Genomics accounts
Customer project accounts
Project support and tools development
PREDEFINED ANALYSES CUSTOM-‐TAILORED ANALYSES
GENOMICS DELIVERY
Deliverables 2014 Consultancy and Training • Con'nuing providing advanced bioinforma'cs support to projects na'on-‐wide and maintaining
(old) and building (new) domain-‐specific competence • Expand into new competence areas (e.g. Integra've bioinforma'cs / Big Data) • Genome annota'on pla7orm used in at least 3 new projects • Delivering success stories within our supported research projects • Drop-‐in bioinforma'cs consultancy at SciLifeLab • Provide advanced training in 10+ courses na'on-‐wide
Infrastructure • Provision of a respository of good/useful scripts • Secure system for compute and storage Mosler • Produc'on system for SciLifeLab pla7orms, providing redundant HPC resources w/ high availability • User-‐friendly interface towards UPPNEX compute resources • Prototype system for cloud compu'ng in bioinforma'cs
Interna8onal • Integra'on of the Human Protein Atlas (HPA) into ELIXIR as Swedish node contribu'on • Hos'ng the European ELIXIR Heads-‐of-‐Nodes mee'ng in May
Organisa8onal • Integrate all ac'vi'es as a Na'onal Bioinforma'cs Infrastructure; Regular pla7orm mee'ngs • Coordina'on mee'ngs with genomics pla7orms
Bioinforma'cs Pla7orm provides custom-‐tailored analyses
• Study design consulta'on (free)
support@bils.se
• Short-‐term support (≤80h; free; first come first serve) • Medium-‐term support (>80h; user fee; first come first serve)
hjp://bils.se/resources/suppor7orm/index.php • Long-‐term support (500h; free: scien'fic evalua'on)
hjp://www.scilifelab.se/facili'es/wabi/
• Compute and storage (free; majority of hardware and system administra'on belongs to SNIC) hjp://www.uppmax.uu.se/
Next deadline for applica'ons Feb 27!
Growth (Numbers from BILS)
0
100
200
300
400
500
600
700
800
900
1000
2011 2012 2013 2014 2015 2016 2017 2018
Staff
Projects
PI
Distribu8on of PIs in projects in 2013
KI, 38
UU, 37
SU, 17
KTH, 9
GU, 28 LU, 28
UmU, 23
LiU, 22
NRM, 22
SLU, 11
Chalmers, 6 Sahlgrenska University
Hospital, 3
NGI, 2
AstraZeneca, 1 FOI, 1 LTH, 1 Norrlands Universitetssjukhus, 1 Polismyndigheten, 1
SVA, 1 WABI, 1 ÖrU, 1
~400 short-‐term projects/year ~20 long-‐term projects/year
2014: Over 450 ac've projects from all over Sweden
2004 2005 2006 2007 2008 2009 2010 2011 2012 2013
100
200
300
400 Active Projects
Num
ber o
f act
ive p
roje
cts
●
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UPPMAXUPPNEX
Other research fields
Integrated in Swedish e-‐Science infrastructure
2014: Over 450 ac've projects from all over Sweden
Large sequencing projects use UPPNEX
Short-‐term Support and Infrastructure BILS – Bioinforma8cs Infrastructure for Life Sciences
www.scilifelab.se/facili8es/bils/
Bengt Mikael Fredrik Persson Borg Levander
Technical Proteomics Director coordinator coordinator • BILS is a distributed national research
infrastructure supported by the Swedish Research Council (VR) • Nodes at each of the 6 large univerisities • Coordination with other bioinformatics activities • Training activities, annual symposium/user meeting
• BILS provides • Support/Consultancy (“human eCloud” for life sciences)
80 hours for free, additional hours for a subsidised fee • Databases and software tools
Computing and storage in collaboration with SNIC
• BILS coordinates the Swedish node in the European infrastructure for biological information ELIXIR
• Annual budget ~3.5 MEUR (2014)
• ~2.2 MEUR from Swedish Research Council • ~1.3 MEUR from SciLifeLab and
participating universities
Syst. development Training Genomics coordinators coordinator coordinator
Magnus Henrik Jonas Sara Alm-Rosenblad Lantz Hagberg Light
Long-‐term Support Wallenberg Advanced Bioinforma8cs Infrastructure
www.scilifelab.se/facili8es/wabi/
Björn Nystedt Thomas Svensson
Tailored solu-ons – high impact
Siv Andersson Gunnar von Heijne
Applied bioinforma'cs: 500h free support/project • Variant analyses in health and disease • Transcriptomics • Novel genomes • Metagenomics
Directors
Managers Swedens strongest unit for analyses of large-‐scale genomic data (13 FTE, increasing)
Na'onal commijee reviews and selects projects based on scien'fic quality
Annota'on is a complex, 'me-‐consuming process
Producing an annota'on for a vertebrate genome can take months
Requires both experience and computa'onal infrastructure
Which data do I combine in what ways to achieve op'mal results?
What pipelines are available and how do I set them up?
What computa'onal resources are required? Do I have the capability to develop custom solu'ons if my data requires it?
Is using my grant money to train someone a good long-‐term investment for me?
The BILS genome annota8on and assembly plaQorm
Teaching
www.scilifelab.se/educa'on/courses/
2015-‐04-‐07 -‐ 2015-‐04-‐09, Course | Uppsala RNA-‐seq, 1 hp 2015-‐04-‐27 -‐ 2015-‐04-‐28, Course | Uppsala Introduc8on to Genome Annota8on, 1 hp 2015-‐05-‐18 -‐ 2015-‐05-‐23, Course | Uppsala Perl Programming with Applica8on to Bioinforma8cs, 2 hp
The Swedish Bioinforma'cs Advisory Program
A new teaching model, where PhD students get a senior bioinforma'cian as a personal advisor during 2 years of their PhD. Three grand mee'ngs per year with all the students, and their advisors and PhD supervisors, to aid networking and knowledge transfer. First call late 2014: >50 applicants for 15 places Next call late 2015 www.scilifelab.se/educa'on/mentorship/the-‐swedish-‐bioinforma'cs-‐advisory-‐program/
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